Conserved Non-Pocket Interactions Drive The Diversity Of Peptide Presentation By Mhc Class I Molecules

Author

Kyle Jackson, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical SciencesFollow

Author ORCID Identifier

https://orcid.org/0000-0002-3711-2861

Date of Graduation

8-2021

Document Type

Dissertation (PhD)

Program Affiliation

Immunology

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Gregory Lizee

Committee Member

Jagannadha K Sastry

Committee Member

Juan Fueyo

Committee Member

Gheath Al-Atrash

Committee Member

Pamela L Wenzel

Abstract

Cytotoxic T-lymphocytes (CTL) can lyse infected or transformed cells through recognition of peptides presented on human leukocyte antigen (HLA) molecules. A thorough understanding of peptide-HLA interactions is needed for improvement of CTL-based immunotherapies. We observed that aspartic acid (D) and glutamic acid (E) at peptide position 4 are highly prevalent in HLA-I peptide ligands, and discovered that they interact with arginine (R) in position 65 and lysine (L) in position 66 of the α1 helix of the binding groove in HLA-A*0201 and HLA-A*2402. Since this interaction differed from well-characterized peptide-HLA anchor interactions mediated by peptide position 2 and the C-terminus, we investigated if the charged interactions between D/E in position 4 and R65 and K66 on the α1 helix of A*0201 and A*2402 are important for peptide antigen presentation. Mutations to R65 and K66 caused loss of HLA cell surface expression, reduced peptide repertoire diversity, and loss of charged interactions between D/E4 and p65-66 in both A*0201 and A*2402. In addition, mutating R65 and/or K66 altered the peptide motifs of both A*0201 and A*2402 specifically in peptide positions 1, 2 and the C-terminus. Peptide binding and stability assays revealed that D/E residues in position 4 contribute significantly to both peptide binding and stability, particularly in peptides with weaker N and C-terminal anchors. Several other HLA-I alleles and MHC molecules from different animal species also showed conservation of R65 and K66, in addition to D/E4 in bound peptide ligands, suggesting that charged interactions between D/E4 and R65/K66 represent a conserved, non-canonical pan-MHC-I anchor interaction that should be accounted for when identifying peptide targets for immunotherapies.

Keywords

Antigen presentation, Human Leukocyte Antigens, HLA Class I, peptide binding stability, mass spectrometry, computational modeling, immunopeptidome, peptide repertoire diversity, molecular interactions, molecular dynamics